{ "type": "genome", "identifier": "GCF_000258495.1", "organism": "Pedobacter agri PB92", "title": "Pedobacter agri PB92", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Korea Basic Science Institute (KBSI)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000258495.1", "bioproject": "PRJNA224116", "biosample": "SAMN02470139", "wgs_master": "AJLG00000000.1", "refseq_category": "na", "taxid": "1149865", "species_taxid": "454586", "organism_name": "Pedobacter agri PB92", "infraspecific_name": "strain=PB92", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/04/11", "asm_name": "PB92_1.0", "asm_submitter": "Korea Basic Science Institute (KBSI)", "gbrs_paired_asm": "GCA_000258495.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/258/495/GCF_000258495.1_PB92_1.0", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5141552", "genome_size_ungapped": "5141552", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "379", "contig_count": "379", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000258495.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4874", "protein_coding_gene_count": "4668", "non_coding_gene_count": "55", "pubmed_id": "22740666" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-04-11", "dateModified": "2012-04-11", "datePublished": "2012-04-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter agri PB92" ], "sample_taxid": [ "1149865" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Daejeon" ], "sample_host_location_id": [], "data_size": "1.460 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5141552", "Number of Sequences": "379", "Longest Sequences (bp)": "118974", "N50 (bp)": "25419", "Gap Ratio (%)": "0.000019", "GCcontent (%)": "38.0", "Number of CDSs": "4410", "Average Protein Length": "306.0", "Coding Ratio (%)": "78.7", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter agri", "strain": "strain=PB92", "accession": "GCA_000258495.1", "taxid": 454586, "species_taxid": 454586, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1515, "total_fragments": 1533, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter frigidisoli", "strain": "strain=RP-3-11", "accession": "GCA_004331675.1", "taxid": 2530455, "species_taxid": 2530455, "relation_to_type": "type", "validated": true, "ani": 80.8893, "matched_fragments": 692, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter chinensis", "strain": "strain=JDX94", "accession": "GCA_003339865.1", "taxid": 2282421, "species_taxid": 2282421, "relation_to_type": "type", "validated": true, "ani": 80.7572, "matched_fragments": 752, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter borealis", "strain": "strain=DSM 19626", "accession": "GCA_000708285.2", "taxid": 475254, "species_taxid": 475254, "relation_to_type": "type", "validated": true, "ani": 80.4871, "matched_fragments": 601, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter kyonggii", "strain": "strain=K-4-11-1", "accession": "GCA_004310665.1", "taxid": 1926871, "species_taxid": 1926871, "relation_to_type": "type", "validated": true, "ani": 80.3565, "matched_fragments": 656, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrotolerans", "strain": "strain=CGMCC 1.15644", "accession": "GCA_014643495.1", "taxid": 1843235, "species_taxid": 1843235, "relation_to_type": "type", "validated": true, "ani": 80.3517, "matched_fragments": 642, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ginsenosidimutans", "strain": "strain=KACC 14530", "accession": "GCA_001442625.1", "taxid": 687842, "species_taxid": 687842, "relation_to_type": "type", "validated": true, "ani": 80.3231, "matched_fragments": 682, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrotolerans", "strain": "strain=DSM 103236", "accession": "GCA_004340665.1", "taxid": 1843235, "species_taxid": 1843235, "relation_to_type": "type", "validated": true, "ani": 80.3156, "matched_fragments": 645, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_003664035.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 80.2992, "matched_fragments": 615, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ghigonis", "strain": "strain=Marseille-Q2390", "accession": "GCA_903166585.1", "taxid": 2730403, "species_taxid": 2730403, "relation_to_type": "type", "validated": true, "ani": 80.2919, "matched_fragments": 571, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_004402005.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 80.2808, "matched_fragments": 614, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter petrophilus", "strain": "strain=LMG 29686", "accession": "GCA_009674725.1", "taxid": 1908241, "species_taxid": 1908241, "relation_to_type": "type", "validated": true, "ani": 80.2672, "matched_fragments": 609, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter fastidiosus", "strain": "strain=CCM 8938", "accession": "GCA_014306625.1", "taxid": 2765361, "species_taxid": 2765361, "relation_to_type": "type", "validated": true, "ani": 80.2665, "matched_fragments": 650, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter kyungheensis", "strain": "strain=KACC 16221", "accession": "GCA_000812965.1", "taxid": 1069985, "species_taxid": 1069985, "relation_to_type": "type", "validated": true, "ani": 80.1375, "matched_fragments": 592, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter terrae", "strain": "strain=DSM 17933", "accession": "GCA_900100705.1", "taxid": 405671, "species_taxid": 405671, "relation_to_type": "type", "validated": true, "ani": 80.1159, "matched_fragments": 591, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter endophyticus", "strain": "strain=JBR3-12", "accession": "GCA_015679185.1", "taxid": 2789740, "species_taxid": 2789740, "relation_to_type": "type", "validated": true, "ani": 79.778, "matched_fragments": 545, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter conchicola", "strain": "strain=MYSH2", "accession": "GCA_003432115.1", "taxid": 2303333, "species_taxid": 2303333, "relation_to_type": "type", "validated": true, "ani": 76.3639, "matched_fragments": 69, "total_fragments": 1533, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000258495.1", "gtdb_species": "s__Pedobacter agri", "ani": 100.0, "matched_fragments": 1515, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_004210715.1", "gtdb_species": "s__Pedobacter sp004210715", "ani": 83.3889, "matched_fragments": 687, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001422545.1", "gtdb_species": "s__Pedobacter sp001422545", "ani": 81.379, "matched_fragments": 798, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_004331675.1", "gtdb_species": "s__Pedobacter sp004331675", "ani": 80.8794, "matched_fragments": 692, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003339865.1", "gtdb_species": "s__Pedobacter chinensis", "ani": 80.7533, "matched_fragments": 752, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000708265.2", "gtdb_species": "s__Pedobacter sp000708265", "ani": 80.3938, "matched_fragments": 622, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003688475.1", "gtdb_species": "s__Pedobacter sp003688475", "ani": 80.3866, "matched_fragments": 616, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_004310665.1", "gtdb_species": "s__Pedobacter kyonggii", "ani": 80.3515, "matched_fragments": 657, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_004340665.1", "gtdb_species": "s__Pedobacter psychrotolerans", "ani": 80.3183, "matched_fragments": 644, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004342125.1", "gtdb_species": "s__Pedobacter sp004342125", "ani": 80.3157, "matched_fragments": 639, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.29", "min_intra_species_ani": "95.29", "mean_intra_species_af": 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"num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_005938645.2", "gtdb_species": "s__Pedobacter sp005938645", "ani": 80.2521, "matched_fragments": 638, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003173575.1", "gtdb_species": "s__Pedobacter paludis", "ani": 80.2247, "matched_fragments": 649, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { 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"s__Pedobacter sp001027745", "ani": 80.0452, "matched_fragments": 536, "total_fragments": 1533, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": 0.477, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 25.0, "optimum_ph": 7.0, "genome_size": 5141552.0, "gc_content": 42.651, "coding_genes": 4725.333, "rRNA16S_genes": 4.333, "tRNA_genes": 57.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.281, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.5, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.5, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "agri", "PB92" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }